The influence of orthodontic tooth movement with diminished periodontal support is unclear. The aim of the present study was to evaluate bone healing in surgical defects following orthodontic tooth movement with and without periodontal ligament (PDL) and root surface damage. The study comprised 33 adult male Wistar rats, divided into two groups: group 1 (n = 14) with bony defect and no root damage and group 2 (n = 19) with periodontal bony defect including root/PDL damage on the mesial root of the maxillary first molar. One week after a surgical defect was created, orthodontic protraction of the right maxillary first molar was initiated in both groups. After 2 weeks of protraction, retention of 1 week was established; at the end of this period block sections were made. Histomorphometric analysis through light microscopy of decalcified tissue was performed. Results were statistically analyzed using independent samples t test and analysis of variance (ANOVA) with repeated measures. Differences between groups in total area of bone defect and bone apposition were not statistically significant. Bone apposition calculated as percentage of the bone defect was significantly (t-test) greater (P = 0.002) in group 2 (46.21%) than in group 1 (24.95%). Within each group, area of bone apposition was significantly (ANOVA) greater in the distal than in the mesial quadrants of the bony defect (P = 0.006) and in the apical than the occlusal ones (P = 0.021). Following orthodontic tooth movement, periodontal bony defects showed enhanced bony healing compared with alveolar bone defects with no direct association with the periodontal attachment apparatus.